NPTN neuroplastin [Homo sapiens (human)] - Gene

Summary

Official Symbol: NPTNprovided by HGNC
Official Full Name: neuroplastinprovided by HGNC
Primary source: HGNC:HGNC:17867
See related: Ensembl:ENSG00000156642 MIM:612820; AllianceGenome:HGNC:17867
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: GP55; GP65; SDR1; np55; np65; SDFR1
Summary: This gene encodes a type I transmembrane protein belonging to the Ig superfamily. The protein is believed to be involved in cell-cell interactions or cell-substrate interactions. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2009]
Expression: Ubiquitous expression in brain (RPKM 67.5), endometrium (RPKM 61.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q24.1

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (73560014..73633389, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (71377168..71450559, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (73852355..73925730, complement)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Hippocampal expression of neuroplastin is altered in Alzheimer's disease.
Title: Hippocampal expression of cell-adhesion glycoprotein neuroplastin is altered in Alzheimer's disease.
Expression profiling of NPTNbeta showed significantly high expression levels in lung cancer cell lines. NPTNbeta has strong ability to induce cancer-related cellular events, including anchorage-independent growth, motility and invasiveness, in lung cancer cells in response to extracellular S100A8/A9, eventually leading to the expression of a cancer disseminative phenotype in lung tissue in vivo.
Title: Neuroplastin-β mediates S100A8/A9-induced lung cancer disseminative progression.
these results indicate that epilation induces McSCs activation through EDN3/EDNRB signaling and in turn leads to skin and hair hyperpigmentation. The findings suggest that EDN/EDNRB signaling may serve as a potential therapeutic target to promote repigmentation in hypopigmentation disorders.
Title: Neuroplastin deletion in glutamatergic neurons impairs selective brain functions and calcium regulation: implication for cognitive deterioration.
Cryoelectron microscopy structure offers important insight into how the NPTN binds to the PMCA1.
Title: Structure of the human plasma membrane Ca(2+)-ATPase 1 in complex with its obligatory subunit neuroplastin.
Xkr8-BSG/NPTN complex is required for phosphatidylserine scrambling in apoptotic cell membranes.
Title: Xkr8 phospholipid scrambling complex in apoptotic phosphatidylserine exposure.
This study showed that Single nucleotide polymorphism in the neuroplastin locus associates with cortical thickness and intellectual ability in adolescents.
Title: Single nucleotide polymorphism in the neuroplastin locus associates with cortical thickness and intellectual ability in adolescents.
correct synaptic membrane protein localization, neuronal energy supply, expression of LTP and LTD, animal and human behaviour, and pathophysiology and disease--{review}
Title: The Neuroplastin adhesion molecules: key regulators of neuronal plasticity and synaptic function.
NPTN may be involved in genetic susceptibility to schizophrenia.
Title: Association study of putative promoter polymorphisms in the neuroplastin gene and schizophrenia.
In human brain np65 is prominently present in cerebellum while np55 is the predominant isoform in mouse and rat cerebellum.
Title: The immunolocalization of the synaptic glycoprotein neuroplastin differs substantially between the human and the rodent brain.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH101954 (e-PCR)
- UniSTS:96289

D15S1086 (e-PCR)
- UniSTS:28206

NoName (e-PCR)
- UniSTS:495154

WI-14402 (e-PCR)
- UniSTS:63820

G31039 (e-PCR)
- UniSTS:54350

MARC_21804-21805:1025095690:1 (e-PCR)
- UniSTS:268634

D1S1423 (e-PCR)
- UniSTS:149619

RH46305 (e-PCR)
- UniSTS:51596

STS-H81048 (e-PCR)
- UniSTS:46246

SHGC-24300 (e-PCR)
- UniSTS:80557

SHGC-149501 (e-PCR)
- UniSTS:182237

D15S904 (e-PCR)
- UniSTS:1505

D15S1291 (e-PCR)
- UniSTS:61936

WI-11717 (e-PCR)
- UniSTS:40692

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cell adhesion molecule binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables type 1 fibroblast growth factor receptor binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in excitatory synapse assembly	IEA Inferred from Electronic Annotation more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular calcium ion homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in long-term synaptic potentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cytokine production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cytosolic calcium ion concentration	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of fibroblast growth factor receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of long-term neuronal synaptic plasticity	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of neuron projection development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of receptor localization to synapse	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cell surface	HDA more info	PubMed
located_in immunological synapse	ISS Inferred from Sequence or Structural Similarity more info
located_in postsynaptic density	IEA Inferred from Electronic Annotation more info
located_in presynaptic membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: neuroplastin

Names: SDR-1; stromal cell derived factor receptor 1; stromal cell-derived receptor 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001161363.2 → NP_001154835.1 neuroplastin isoform c precursor

See identical proteins and their annotated locations for NP_001154835.1

Status: REVIEWED

Description

Transcript Variant: This variant (c) uses an alternate in-frame splice site in the 3' coding region compared to variant b. This results in a shorter protein (isoform c), compared to isoform b.

Source sequence(s)

AK297184, AK313441, BC105979, CN357076

Consensus CDS

CCDS58380.1

UniProtKB/Swiss-Prot

Q9Y639

Related

ENSP00000457028.1, ENST00000563691.5

Conserved Domains (3) summary

pfam13927
Location:238 → 320

Ig_3; Immunoglobulin domain

cd00096
Location:32 → 36

Ig; Ig strand A [structural motif]

cl11960
Location:31 → 146

Ig; Immunoglobulin domain
NM_001161364.2 → NP_001154836.1 neuroplastin isoform d precursor

See identical proteins and their annotated locations for NP_001154836.1

Status: REVIEWED

Description

Transcript Variant: This variant (d) lacks an alternate in-frame exon in the 5' coding region and uses an alternate in-frame splice site in the 3' coding region, compared to variant b. This results in a shorter protein (isoform d), compared to isoform b.

Source sequence(s)

BC105979, BC143880, CN357076

Consensus CDS

CCDS58379.1

UniProtKB/Swiss-Prot

Q9Y639

Related

ENSP00000456349.1, ENST00000562924.5

Conserved Domains (3) summary

pfam13927
Location:122 → 204

Ig_3; Immunoglobulin domain

cd00096
Location:139 → 146

Ig; Ig strand B [structural motif]

cl11960
Location:52 → 103

Ig; Immunoglobulin domain
NM_012428.4 → NP_036560.1 neuroplastin isoform b precursor

See identical proteins and their annotated locations for NP_036560.1

Status: REVIEWED

Description

Transcript Variant: This variant (b), alternatively known as beta, represents the longest transcript and encodes the longest isoform (b).

Source sequence(s)

AF109126, AI357728, BC067828, CN357076

Consensus CDS

CCDS10249.1

UniProtKB/Swiss-Prot

B2RAL7, B7Z4D3, B7ZLL2, Q17R52, Q59EJ9, Q6NVX7, Q9Y639, Q9Y640

Related

ENSP00000290401.4, ENST00000345330.9

Conserved Domains (3) summary

pfam13927
Location:238 → 320

Ig_3; Immunoglobulin domain

cd00096
Location:32 → 36

Ig; Ig strand A [structural motif]

cl11960
Location:31 → 146

Ig; Immunoglobulin domain
NM_017455.4 → NP_059429.1 neuroplastin isoform a precursor

See identical proteins and their annotated locations for NP_059429.1

Status: REVIEWED

Description

Transcript Variant: This variant (a), alternatively known as alpha, lacks an alternate in-frame exon, compared to variant b. The resulting isoform (a) is shorter, compared to isoform b.

Source sequence(s)

AI357728, BC067828, CN357076

Consensus CDS

CCDS10250.1

UniProtKB/Swiss-Prot

Q9Y639

Related

ENSP00000342958.6, ENST00000351217.10

Conserved Domains (3) summary

pfam13927
Location:122 → 204

Ig_3; Immunoglobulin domain

cd00096
Location:139 → 146

Ig; Ig strand B [structural motif]

cl11960
Location:52 → 103

Ig; Immunoglobulin domain